The invention discloses a key factor yield contribution calculation method based on a crop growth mechanism. The key factor yield contribution calculation method comprises the following steps: selecting a plurality of crop varieties of different periods in a research site, and determining a respective variety parameter range according to the crop phenology and the yield data of a practical field observation experiment; utilizing the meteorological data and the crop management measure data of the research site to drive an APSIM (Agricultural Production Systems Simulator) crop growth mechanism model, and adopting a trial and error method to determine a specific crop variety parameter value; carrying out comparison analysis on crop growth mechanism model simulation yield values under different varieties and different management measures of a long-time sequence, and independently calculating the contributions of variety change and management measure change on the crop yield; and carrying out linear fitting on the crop yield simulation value of the crop variety on the long-time sequence to calculate the contribution of climatic variation on the crop yield.